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      <li class="navelem"><a class="el" href="namespacemoltk.html">moltk</a>      </li>
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<div class="title">moltk::Alignment Member List</div>  </div>
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This is the complete list of members for <a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a>, including all inherited members.<table>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a85b58270d404b46f62fc7eeed7e2b105">align</a>(const Alignment &amp;, const EString &amp;, const EString &amp;) const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a32d343d192cf39cb0f0968e26223af78">Alignment</a>()</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a880bde0789a4ed97ed7ce9fd238fd71c">Alignment</a>(const Biosequence &amp;sequence)</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a81554da54922ffeae9428824b786b0a3">Alignment</a>(const std::string &amp;alignment_string)</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a42793c08a9b84d49d23d574405b477ea">Alignment</a>(const char *alignment_string)</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#ad319bf0e8fdcb7b2de65fd7d03c7261d">append_sequence</a>(const Biosequence &amp;sequence)</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a3743461184a4c55f0e54e6ade1e9ef68">EString</a> typedef</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a338529e9299d91018d134b130b26a6dd">fasta</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a68e0607cad31d5eec46b90d81c62eed2">get_estring</a>(size_t index) const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a628e15ff3478f591868bc1465109b04d">get_number_of_columns</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a2486341695c895251bd124357a21371c">get_number_of_sequences</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#aa27d71c83a6cb5d0584e9db931119045">get_sequence</a>(size_t index) const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#adc61d7c6de21d88523c96423b2b1f408">id_table</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8">List</a> enum name</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8a64315d2bea93b3770675d3a9bcbcfbbc">LIST_SEQUENCE</a> enum value</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8a9532ce6c3a8fccfd79b37fe279e387e7">LIST_STRUCTURE</a> enum value</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a9fc6acdad2f8dc2e9a070b39dd391533">load_fasta</a>(std::istream &amp;input_stream)</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#aa75592aca10538670c26a05e2ec1dac3">load_fasta</a>(const std::string &amp;file_name)</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a1744a2bb15a68fd5eee6ad9f457f186f">load_string</a>(const std::string &amp;alignment_string)</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#ad7f4499388720ae855277fe046bbea44">m_score</a></td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a5c933bbcecb2459310f897119f11fda7">operator&lt;&lt;</a>(std::ostream &amp;os, const Alignment &amp;ali)</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [friend]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a2574c152a5662243f4626d4bb0de1ed3">pretty</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#adf2beb6028be5a2ab437bb93aff90b61">pretty_width</a></td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a4bac71883cd63ec6b766497640684a81">rows</a></td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#abde767106550bdb46c923146b3629c2f">score</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a78aa4d5f29a114e1a58b7f32eb98e24d">sequences</a></td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a110d140d99982b84a8545a23d51b8543">set_score</a>(const moltk::units::Information &amp;s)</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#aa6fde73aa22498189439380b2a245f37">structures</a></td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a60122a64be28573829c1a956737c8c11">write_fasta</a>(std::ostream &amp;output_stream) const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#afba7a1a9917567751bbe2b1ec68fd4e2">write_fasta</a>(const std::string &amp;file_name) const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a1ade7cd4b169cbf8bc72504cd973a13f">write_id_table</a>(std::ostream &amp;output_stream) const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#ab6e11bdbb183223b74b0937400615fbd">write_id_table</a>(const std::string &amp;file_name) const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a49b02248c0a05137369e26d826b9075f">write_pretty</a>(std::ostream &amp;output_stream) const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#abc791f9f0f43a9be258c8a2f013a682a">write_pretty</a>(const std::string &amp;file_name) const </td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment.html#a7707218270b81f730c8be5d19763dc22">~Alignment</a>()</td><td><a class="el" href="classmoltk_1_1Alignment.html">moltk::Alignment</a></td><td><code> [inline]</code></td></tr>
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